And ,no, it may not affect the on time delivery to the customer most of the time. But the costs involved in searching for the product, staying late to do it for the company, working extra hours to essentially cover for this process (assuming it is more wide spread), if captured properly, can be the data that the warehouse needs to get a better functioning system within the warehouse.
As I said in the past, no external audit and NC's can replace good management. You put yourself, as an auditor, in an impossible situation. Because, as you know very well, the minute you decide to report the issue was an NC, then the protocol is for them to implement corrective action, which means that the problem should not recur. But, as you already agreed, there is no warehouse which can guarantee 100% accuracy:
I agree that there is probably not a warehouse in on the planet that is 100% accurate -otherwise they would not bother with cycle counts etc.
So, how can you deem your NC closed, if there will always be products out of place? Unless, you determine that 99.2% is good enough, or 86% or 73%, before you close the NC. Either way, you as the external auditor would have to determine a minimum level of performance before closing the corrective action request.
Or, the organization at hand simply deletes the requirement from their own command media, so a NC can no longer be justified. Would it make the situation any better?
For me it is clear - its a nonconformance. Its required. It wasnt done.
The only problem with living life in black and white is that thing called reality which tends to come in shades of gray.